Conda install does not properly bundle db dir

[boulund]

It seems the bioconda package does not properly bundle the db folder.

When installing SUPER-FOCUS using pip, you get a folder in your python library folder that contains the db directory from the repo (including the databasePKs.txt and organism2subsystem.txt files, etc.). For example, if I create an empty conda environment named superfocus and use pip to install super-focus into that conda environment, I get the following result:

$ conda create -n superfocus pip
... (install log removed for brevity)

$ conda activate superfocus
(superfocus)$ pip install superfocus
Collecting superfocus
  Downloading superfocus-0.35-py3-none-any.whl (223 kB)
     |████████████████████████████████| 223 kB 5.4 MB/s
Collecting numpy>=1.12.1
  Downloading numpy-1.21.5-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (15.9 MB)
     |████████████████████████████████| 15.9 MB 19.1 MB/s
Collecting scipy>=0.19.0
  Downloading scipy-1.7.3-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (39.9 MB)
     |████████████████████████████████| 39.9 MB 29.2 MB/s
Installing collected packages: numpy, scipy, superfocus
Successfully installed numpy-1.21.5 scipy-1.7.3 superfocus-0.35

(superfocus)$ tree ~/.conda/envs/superfocus/lib/python3.10/site-packages/superfocus_app/
/ceph/home/boulund/.conda/envs/superfocus/lib/python3.10/site-packages/superfocus_app/
├── db
│   ├── database_PKs.txt
│   ├── focus_reduction
│   │   ├── blast
│   │   ├── diamond
│   │   └── rapsearch2
│   ├── organisms2subsystem.txt
│   ├── static
│   │   ├── blast
│   │   ├── diamond
│   │   └── rapsearch2
│   └── tmp
├── do_alignment.py
├── __init__.py
├── __pycache__
│   ├── do_alignment.cpython-310.pyc
│   ├── __init__.cpython-310.pyc
│   ├── superfocus.cpython-310.pyc
│   └── superfocus_downloadDB.cpython-310.pyc
├── superfocus_downloadDB.py
└── superfocus.py

11 directories, 10 files

When installing SUPER-FOCUS via conda, the db folder is not installed, leading to the issues described in https://github.com/metageni/SUPER-FOCUS/issues/67, https://github.com/metageni/SUPER-FOCUS/issues/65, etc. This is what the superfocus_app folder looks like when installing with conda:

$ conda create -n superfocus_conda super-focus
... (install log removed for brevity)

$ conda activate superfocus_conda
(superfocus_conda)$ tree ~/.conda/envs/superfocus_conda/lib/python3.10/site-packages/superfocus_app/
/ceph/home/boulund/.conda/envs/superfocus_conda/lib/python3.10/site-packages/superfocus_app/
├── do_alignment.py
├── __init__.py
├── __pycache__
│   ├── do_alignment.cpython-310.pyc
│   ├── __init__.cpython-310.pyc
│   ├── superfocus.cpython-310.pyc
│   └── superfocus_downloadDB.cpython-310.pyc
├── superfocus_downloadDB.py
└── superfocus.py

1 directory, 8 files

[boulund]

I developed a workaround to enable using SUPER-FOCUS with a conda-based installation, explained in: https://github.com/metageni/SUPER-FOCUS/pull/73#issuecomment-999466528

[metageni]

Thanks @boulund. The PR has been merged and the already created version (1.1) should have the fix.

https://github.com/bioconda/bioconda-recipes/pull/32145